Showing papers in "Journal of Biosciences in 2009"

Human papillomavirus E6 and E7 oncoproteins as risk factors for tumorigenesis

Abstract: Human papillomavirus (HPV) is small, double-stranded DNA virus that infects mucosal and cutaneous epithelial tissue. HPV is sexually transmitted and the viral DNA replicates extrachromosomally. The virus is non-enveloped and has an icosahedral capsid. There are approximately 118 types of HPV, which are characterized as high-risk or lowrisk types. High-risk HPVs cause malignant transformation while the low-risk ones cause benign warts and lesions. The expression of E6 and E7 is normally controlled during the normal viral life cycle when viral DNA replicates extrachromosomally. HPV E6 and E7 oncoproteins are overexpressed when the viral genome integrates into the host DNA. Deregulated overexpression of E6 and E7 oncoproteins can cause several changes in cellular pathways and functions leading to malignant transformation of cells and tumorigenesis. In this review, we focus on several cellular mechanisms and pathways that are altered in the presence of E6 and E7, the target proteins of E6 and E7 inside the host cell and how they contribute to the development of the transformed phenotype.

A simple and efficient Agrobacterium-mediated procedure for transformation of tomato.

Abstract: We describe a highly efficient and reproducible Agrobacterium-mediated transformation protocol applicable to several varieties of tomato (Solanum lycopersicum, earlier known as Lycopersicum esculentum). Conditions such as co-cultivation period, bacterial concentration, concentration of benzyl amino purine (BAP), zeatin and indole acetic acid (IAA) were optimized. Co-cultivation of explants with a bacterial concentration of 108 cells/ml for three days on 2 mg/l BAP, followed by regeneration on a medium containing 1 mg/ml zeatin resulted in a transformation frequency of 41.4%. Transformation of tomato plants was confirmed by Southern blot analysis and β-glucuronidase (GUS) assay. The protocol developed showed very high efficiency of transformation for tomato varieties Pusa Ruby, Arka Vikas and Sioux. The optimized transformation procedure is simple, efficient and does not require tobacco, Petunia, tomato suspension feeder layer or acetosyringone.

Evidence of Late Palaeocene-Early Eocene equatorial rain forest refugia in southern Western Ghats, India

Abstract: Equatorial rain forests that maintain a balance between speciation and extinction are hot-spots for studies of biodiversity. Western Ghats in southern India have gained attention due to high tropical biodiversity and endemism in their southern most area. We attempted to track the affinities of the pollen flora of the endemic plants of Western Ghat area within the fossil palynoflora of late Palaeocene-early Eocene (∼55–50 Ma) sedimentary deposits of western and northeastern Indian region. The study shows striking similarity of extant pollen with twenty eight most common fossil pollen taxa of the early Palaeogene. Widespread occurrences of coal and lignite deposits during early Palaeogene provide evidence of existence of well diversified rain forest community and swampy vegetation in the coastal low lying areas all along the western and northeastern margins of the Indian subcontinent. Prevalence of excessive humid climate during this period has been seen as a result of equatorial positioning of Indian subcontinent, superimposed by a long term global warming phase (PETM and EECO) during the early Palaeogene. The study presents clear evidence that highly diversified equatorial rain forest vegetation once widespread in the Indian subcontinent during early Palaeogene times, are now restricted in a small area as a refugia in the southernmost part of the Western Ghat area. High precipitation and shorter periods of dry months seem to have provided suitable environment to sustain lineages of ancient tropical vegetation in this area of Western Ghats in spite of dramatic climatic changes subsequent to the post India-Asia collision and during the Quaternary and Recent times.

A weak link in metabolism: the metabolic capacity for glycine biosynthesis does not satisfy the need for collagen synthesis.

Abstract: In a previous paper, we pointed out that the capability to synthesize glycine from serine is constrained by the stoichiometry of the glycine hydroxymethyltransferase reaction, which limits the amount of glycine produced to be no more than equimolar with the amount of C 1 units produced. This constraint predicts a shortage of available glycine if there are no adequate compensating processes. Here, we test this prediction by comparing all reported fl uxes for the production and consumption of glycine in a human adult. Detailed assessment of all possible sources of glycine shows that synthesis from serine accounts for more than 85% of the total, and that the amount of glycine available from synthesis, about 3 g/day, together with that available from the diet, in the range 1.5–3.0 g/day, may fall signifi cantly short of the amount needed for all metabolic uses, including collagen synthesis by about 10 g per day for a 70 kg human. This result supports earlier suggestions in the literature that glycine is a semi-essential amino acid and that it should be taken as a nutritional supplement to guarantee a healthy metabolism.

Nanovaccines: recent developments in vaccination

Abstract: In the past 100 years, vaccination has contributed immensely to public health by preventing a number of infectious diseases. Attenuated, killed or part of the microorganism is employed to stimulate the immune system against it. Progress in biotechnology has provided protective immunity through DNA vaccines. In recent years, nanovaccine is a novel approach to the methodology of vaccination. Nanomaterials are delivered in the form of microspheres, nanobeads or micro-nanoprojections. Painless, effective and safe needle-free routes such as the intranasal or the oral route, or patches of microprojections to the skin are some of the approaches which are in the experimental stage at present but may have a great future ahead in nanovaccination.

Retinoblastoma protein: a central processing unit

Abstract: The retinoblastoma protein (pRb) is one of the key cell-cycle regulating proteins and its inactivation leads to neoplastic transformation and carcinogenesis. This protein regulates critical G1-to-S phase transition through interaction with the E2F family of cell-cycle transcription factors repressing transcription of genes required for this cell-cycle check-point transition. Its activity is regulated through network sensing intracellular and extracellular signals which block or permit phosphorylation (inactivation) of the Rb protein. Mechanisms of Rb-dependent cell-cycle control have been widely studied over the past couple of decades. However, recently it was found that pRb also regulates apoptosis through the same interaction with E2F transcription factors and that Rb-E2F complexes play a role in regulating the transcription of genes involved in differentiation and development.

Proteomic analysis of heparin-binding proteins from human seminal plasma: a step towards identification of molecular markers of male fertility.

Abstract: Glycosaminoglycans, especially heparin, are involved in various cell processes such as apoptosis, cell cycle control, platelet activation, capacitation, acrosome reaction and sperm decondensation. Heparin-binding proteins (HBPs) are essential constituents of human seminal fluid, which bind to sperm lipids containing the phosphorylcholine group and mediate the fertilization process. We utilized a proteomic set-up consisting of affinity chromatography, isoelectric focusing (IEF) coupled with matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI TOF/MS) for protein analysis of human HBPs. We resolved 70 different spots on two-dimensional (2-D) gel and subsequently identified these proteins. Forty different types of proteins were identified. Functional analysis revealed that 38% of the proteins belonged to the enzyme category, 20% were involved in RNA processing and transcription, 18% in structure and transport function, and 16% in cell recognition and signal transduction. We also identified 8% of proteins with unknown functions, although their expression in seminal fluid has been documented. Proteins of seminal fluid that bind heparin may be directly involved in sperm capacitation and acrosome reaction (AR), which are the two critical steps for fertilization. This information on HBPs would be useful for identifying potential biomarkers of fertility in the near future.

Deccan volcanism, the KT mass extinction and dinosaurs

Abstract: Recent advances in Deccan volcanic studies indicate three volcanic phases with the phase-1 at 67.5 Ma followed by a 2 m.y. period of quiescence. Phase-2 marks the main Deccan volcanic eruptions in Chron 29r near the end of the Maastrichtian and accounts for ∼80% of the entire 3500 m thick Deccan lava pile. At least four of the world’s longest lava flows spanning 1000 km across India and out into the Gulf of Bengal mark phase-2. The final phase-3 was smaller, coincided with the early Danian Chron 29n and also witnessed several of the longest lava flows.

MMP-1 polymorphism and its relationship to pathological processes.

Abstract: Matrix metalloproteinases (MMPs) are a family of zinc (Zn)-dependent endopeptidases that are collectively capable of cleaving virtually all extracellular matrix (ECM) substrates and play an important role in diverse physiological and pathological processes. The activity of MMPs is regulated at multiple levels. The transcriptional regulation of MMP appears to represent the key step in MMP regulation. There are diverse types of MMPs that differ structural and functionally. MMP-1 is the most ubiquitously expressed interstitial collagenase and has a prominent role in initial cleavage of the ECM. The level of MMP-1 expression can be infl uenced by different single-nucleotide polymorphisms (SNPs) in the promoter region. A functional polymorphism at position −1607 has been shown to alter the transcriptional activity of MMP-1 and was associated with diverse pathological processes. The aim of our review was to discuss some topics related to MMP in physiological and pathological processes, with a focus on MMP-1 polymorphism.

The out-of-India hypothesis: what do molecules suggest?

Abstract: The remarkable geological and evolutionary history of peninsular India has generated much interest in the patterns and processes that might have shaped the current distributions of its endemic biota. In this regard the “Out-of-India” hypothesis, which proposes that rafting peninsular India carried Gondwanan forms to Asia after the break-up of Gondwana super continent, has gained prominence. Here we have reviewed molecular studies undertaken on a range of taxa of supposedly Gondwanan origin to better understand the Out-of-India scenario. This re-evaluation of published molecular studies indicates that there is mounting evidence supporting Out-of-India scenario for various Asian taxa. Nevertheless, in many studies the evidence is inconclusive due to lack of information on the age of relevant nodes. Studies also indicate that not all Gondwanan forms of peninsular India dispersed out of India. Many of these ancient lineages are confined to peninsular India and therefore are relict Gondwanan lineages. Additionally, for some taxa an “Into India” rather than “Out-of-India” scenario better explains their current distribution. To identify the “Out-of-India” component of Asian biota it is imperative that we understand the complex biogeographical history of India. To this end, we propose three oversimplified yet explicit phylogenetic predictions. These predictions can be tested through the use of molecular phylogenetic tools in conjunction with palaeontological and geological data.

Epigenetic learning in non-neural organisms

Abstract: Learning involves a usually adaptive response to an input (an external stimulus or the organism℉s own behaviour) in which the input-response relation is memorized; some physical traces of the relation persist and can later be the basis of a more effective response. Using toy models we show that this characterization applies not only to the paradigmatic case of neural learning, but also to cellular responses that are based on epigenetic mechanisms of cell memory. The models suggest that the research agenda of epigenetics needs to be expanded.

Rapid aggregation and assembly in aqueous solution of Aβ (25–35) peptide

Abstract: The highly toxic A beta (25-35) is a peculiar peptide that differs from all the other commonly studied beta-amyloid peptides because of its extremely rapid aggregation properties and enhanced neurotoxicity. We investigated A beta (25-35) aggregation in H2O at pH 3.0 and at pH 7.4 by means of in-solution analyses. Adopting UV spectroscopy, Congo red spectrophotometry and thioflavin T fluorimetry, we were able to quantify, in water, the very fast assembling time necessary for A beta (25-35) to form stable insoluble aggregates and their ability to seed or not seed fibril growth. Our quantitative results, which confirm a very rapid assembly leading to stable insoluble aggregates of A beta (25-35) only when incubated at pH 7.4, might be helpful for designing novel aggregation inhibitors and to shed light on the in vivo environment in which fibril formation takes place.

BRCA1 and BRCA2 germline mutation analysis among Indian women from south India: identification of four novel mutations and high-frequency occurrence of 185delAG mutation.

Abstract: Mutations in the BRCA1 and BRCA2 genes profoundly increase the risk of developing breast and/or ovarian cancer among women. To explore the contribution of BRCA1 and BRCA2 mutations in the development of hereditary breast cancer among Indian women, we carried out mutation analysis of the BRCA1 and BRCA2 genes in 61 breast or ovarian cancer patients from south India with a positive family history of breast and/or ovarian cancer. Mutation analysis was carried out using conformation-sensitive gel electrophoresis (CSGE) followed by sequencing. Mutations were identified in 17 patients (28.0%); 15 (24.6%) had BRCA1 mutations and two (3.28%) had BRCA2 mutations. While no specific association between BRCA1 or BRCA2 mutations with cancer type was seen, mutations were more often seen in families with ovarian cancer. While 40% (4/10) and 30.8% (4/12) of families with ovarian or breast and ovarian cancer had mutations, only 23.1% (9/39) of families with breast cancer carried mutations in the BRCA1 and BRCA2 genes. In addition, while BRCA1 mutations were found in all age groups, BRCA2 mutations were found only in the age group of ≤40 years. Of the BRCA1 mutations, there were three novel mutations (295delCA; 4213T→A; 5267T→G) and three mutations that have been reported earlier. Interestingly, 185delAG, a BRCA1 mutation which occurs at a very high frequency in Ashkenazi Jews, was found at a frequency of 16.4% (10/61). There was one novel mutation (4866insT) and one reported mutation in BRCA2. Thus, our study emphasizes the importance of mutation screening in familial breast and/or ovarian cancers, and the potential implications of these findings in genetic counselling and preventive therapy.

Palynoflora from Deccan volcano-sedimentary sequence (Cretaceous-Palaeogene transition) of central India: implications for spatio-temporal correlation.

Abstract: The sedimentary beds associated with Deccan Continental Flood Basalt (DCFB) sequences exposed in the volcanic subprovinces of Jabalpur-Mandla-Chhindwara (JMC) regions of Madhya Pradesh and Nand-Dongargaon (N-D) basin and the adjoining areas to the west in Yeotmal-Nanded in Maharashtra were studied for their palynofloral analysis. The sediments were characterized palynologically and changes in the palynoflora are observed at different stratigraphic levels in a number of sections including several new intertrappean localities recorded in recent years. For the purpose of effective correlation of different subprovinces, palynofloras of some of the previously studied intertrappeans are also reviewed. Our studies suggest that before the start of the Deccan volcanic activity, the palynoflora found in the Lameta sediments, was dominated by gymnosperms-angiosperm association. The plant canopy consisted mainly of gymnosperms (Conifers and Podocarpaceae) whereas, the understory members were mostly of palms and herbs (Poaceae and Asteraceae). The eruption of Deccan volcanic flows severely affected the existing floral association and proved fatal for the well established plant community. The immediately overlying sediments associated with the earliest volcanic flows are dominated by pteridophytes and angiosperm taxa (Azolla cretacea, Aquilapollenites bengalensis, Ariadnaesporites sp., Gabonisporis vigourouxii and Triporoletes reticulatus). Higher up in the stratigraphic sequence, similar forms continued with simultaneous appearance of new taxa including Scabrastephanocolpites spp. At still higher stratigraphic levels, abundance of fungi especially the mycorrhizal fungi, concurrent with sharp decline in pollen/spore recovery was observed. In the culminating phase (i.e. Palaeocene) of Deccan volcanic history a new palynofloral assemblage of typical Palaeocene taxa (Dandotiaspora dilata, D. pseudoauriculata, D. plicata, Spinizonocolpites echinatus, Matanomadhiasulcites sp., and Lakiapollis ovatus) was encountered.

Thermal stability of α-amylase in aqueous cosolvent systems

Abstract: The activity and thermal stability of alpha-amylase were studied in the presence of different concentrations of trehalose, sorbitol, sucrose and glycerol. The optimum temperature of the enzyme was found to be 50 +/- 2 degrees C. Further increase in temperature resulted in irreversible thermal inactivation of the enzyme. In the presence of cosolvents, the rate of thermal inactivation was found to be significantly reduced. The apparent thermal denaturation temperature (Tm) app and activation energy (Ea) of alpha-amylase were found to be significantly increased in the presence of cosolvents in a concentration-dependent manner. In the presence of 40% trehalose, sorbitol, sucrose and glycerol, increments in the (Tm)app were 20 degrees C, 14 degrees C, 13 degrees C and 9 degrees C, respectively. The Ea of thermal denaturation of alpha-amylase in the presence of 20% (w/v) trehalose, sorbitol, sucrose and glycerol was found to be 126, 95, 90 and 43 kcal/mol compared with a control value of 40 kcal/mol. Intrinsic and 8-anilinonaphathalene-1-sulphonic acid (ANS) fluorescence studies indicated that thermal denaturation of the enzyme was accompanied by exposure of the hydrophobic cluster on the protein surface. Preferential interaction parameters indicated extensive hydration of the enzyme in the presence of cosolvents.

Odour avoidance learning in the larva of Drosophila melanogaster.

Abstract: Drosophila larvae can be trained to avoid odours associated with electric shock. We describe here, an improved method of aversive conditioning and a procedure for decomposing learning retention curve that enables us to do a quantitative analysis of memory phases, short term (STM), middle term (MTM) and long term (LTM) as a function of training cycles. The same method of analysis when applied to learning mutants dunce, amnesiac, rutabaga and radish reveals memory deficits characteristic of the mutant strains.

Nitrilase-catalysed conversion of acrylonitrile by free and immobilized cells of Streptomyces sp.

Abstract: The biotransformation of acrylonitrile was investigated using thermophilic nitrilase produced from a new isolate Streptomyces sp. MTCC 7546 in both the free and immobilized state. Under optimal conditions, the enzyme converts nitriles to acids without the formation of amides. The whole cells of the isolate were immobilized in agar-agar and the beads so formed were evaluated for 25 cycles at 50°C. The enzyme showed a little loss of activity during reuse. Seventy-one per cent of 0.5 M acrylonitrile was converted to acid at 6 h of incubation at a very low density of immobilized cells, while 100% conversion was observed at 3 h by free cells.

Cell state switching factors and dynamical patterning modules: complementary mediators of plasticity in development and evolution

Abstract: Ancient metazoan organisms arose from unicellular eukaryotes that had billions of years of genetic evolution behind them. The transcription factor networks present in single-celled ancestors at the origin of the Metazoa (multicellular animals) were already capable of mediating the switching of the unicellular phenotype among alternative states of gene activity in response to environmental conditions. Cell differentiation, therefore, had its roots in phenotypic plasticity, with the ancient regulatory proteins acquiring new targets over time and evolving into the “developmental transcription factors” (DTFs) of the “developmental-genetic toolkit.” In contrast, the emergence of pattern formation and morphogenesis in the Metazoa had a different trajectory. Aggregation of unicellular metazoan ancestors changed the organisms’ spatial scale, leading to the first “dynamical patterning module” (DPM): cell-cell adhesion. Following this, other DPMs (defined as physical forces and processes pertinent to the scale of the aggregates mobilized by a set of toolkit gene products distinct from the DTFs), transformed simple cell aggregates into hollow, multilayered, segmented, differentiated and additional complex structures, with minimal evolution of constituent genes. Like cell differentiation, therefore, metazoan morphologies also originated from plastic responses of cells and tissues. Here we describe examples of DTFs and most of the important DPMs, discussing their complementary roles in the evolution of developmental mechanisms. We also provide recently characterized examples of DTFs in cell type switching and DPMs in morphogenesis of avian limb bud mesenchyme, an embryo-derived tissue that retains a high degree of developmental plasticity.

Replica-moulded polydimethylsiloxane culture vessel lids attenuate osmotic drift in long-term cell cultures

Abstract: An imbalance in medium osmolarity is a determinant that affects cell culture longevity. Even in humidified incubators, evaporation of water leads to a gradual increase in osmolarity over time. We present a simple replica-moulding strategy for producing self-sealing lids adaptable to standard, small-size cell-culture vessels. They are made of polydimethylsiloxane (PDMS), a flexible, transparent and biocompatible material, which is gas-permeable but largely impermeable to water. Keeping cell cultures in a humidified 5% CO2 incubator at 37°C, medium osmolarity increased by +6.86 mosmol/kg/day in standard 35 mm Petri dishes, while PDMS lids attenuated its rise by a factor of four to changes of +1.72 mosmol/kg/day. Depending on the lid membrane thickness, pH drifts at ambient CO2 levels were attenuated by a factor of 4 to 9. Comparative evaporation studies at temperatures below 60°C yielded a 10-fold reduced water vapour flux of 1.75 g/day/dm2 through PDMS lids as compared with 18.69 g/day/dm2 with conventional Petri dishes. Using such PDMS lids, about 2/3 of the cell cultures grew longer than 30 days in vitro. Among these, the average survival time was 69 days with the longest survival being 284 days under otherwise conventional cell culture conditions.

Influenza A (H1N1) 2009: a pandemic alarm.

Abstract: At this critical juncture when the world has not yet recovered from the threat of avian influenza, the virus has returned in the disguise of swine influenza, a lesser known illness common in pigs. It has reached pandemic proportions in a short time span with health personnel still devising ways to identify the novel H1N1 virus and develop vaccines against it. The H1N1 virus has caused a considerable number of deaths within the short duration since its emergence. Presently, there are no effective methods to contain this newly emerged virus. Therefore, a proper and clear insight is urgently required to prevent an outbreak in the future and make preparations that may be planned well in advance. This review is an attempt to discuss the historical perspective of the swine flu virus, its epidemiology and route of transmission to better understand the various control measures that may be taken to fight the danger of a global pandemic.

Ageing and cancer as diseases of epigenesis

Abstract: Cancer and ageing are often said to be diseases of development. During the past fifty years, the genetic components of cancer and ageing have been intensely investigated since development, itself, was seen to be an epiphenomenon of the genome. However, as we have learned more about the expression of the genome, we find that differences in expression can be as important as differences in alleles. It is easier to inactivate a gene by methylation than by mutation, and given that appropriate methylation is essential for normal development, one can immediately see that diseases would result as a consequence of inappropriate epigenetic methylation. While first proposed by Boris Vanyushin in 1973, recent studies have confirmed that inappropriate methylation not only causes diseases, and it also may be the critical factor in ageing and cancers.

Single-nucleotide polymorphisms in peroxisome proliferator-activated receptor γ and their association with plasma levels of resistin and the metabolic syndrome in a South Indian population.

Abstract: Studies on the association of the Pro12Ala and C1431T polymorphisms of PPARγ with diabetes and obesity have revealed extensive population-dependent variations. However, association of these polymorphisms with the metabolic syndrome and its individual components has not been well investigated in the Indian population. The Indian population harbours the maximum number of diabetics in the world who are thus more susceptible to metabolic disorders. We screened a South Indian population (N = 699) for a possible association of these polymorphisms with the metabolic syndrome (MS) and type 2 diabetes. We also investigated the correlation of these two single-nucleotide polymorphisms (SNPs) with plasma resistin levels. The C1431T SNP was associated with higher levels of plasma resistin (P = 0.017). Furthermore, C1431T was associated with resistin in different tertiles. Prevalence of the ‘Pro-C’ haplotype decreased with increasing tertiles of resistin (84.1% to 75.4%, P = 0.037). Plasma resistin levels were not found to be associated with MS and type 2 diabetes. These results point to a likely association of plasma resistin levels with PPARγ polymorphisms in the Indian population.

Phenotypic plasticity and longevity in plants and animals: cause and effect?

Abstract: Immobile plants and immobile modular animals outlive unitary animals. This paper discusses competing but not necessarily mutually exclusive theories to explain this extreme longevity, especially from the perspective of phenotypic plasticity. Stem cell immortality, vascular autonomy, and epicormic branching are some important features of the phenotypic plasticity of plants that contribute to their longevity. Monocarpy versus polycarpy can also influence the kind of senescent processes experienced by plants. How density-dependent phenomena affecting the establishment of juveniles in these immobile organisms can influence the evolution of senescence, and consequently longevity, is reviewed and discussed. Whether climate change scenarios will favour long-lived or short-lived organisms, with their attendant levels of plasticity, is also presented.

Functional adaptation and phenotypic plasticity at the cellular and whole plant level

Abstract: The ability to adaptively alter morphological, anatomical, or physiological functional traits to local environmental variations using external environmental cues is especially well expressed by all terrestrial and most aquatic plants. A ubiquitous cue eliciting these plastic phenotypic responses is mechanical perturbation (MP), which can evoke dramatic differences in the size, shape, or mechanical properties of conspecifics. Current thinking posits that MP is part of a very ancient “stress-perception response system” that involves receptors located at the cell membrane/cell wall interface capable of responding to a broad spectrum of stress-inducing factors. This hypothesis is explored here from the perspective of cell wall evolution and the control of cell wall architecture by unicellular and multicellular plants. Among the conclusions that emerge from this exploration is the perspective that the plant cell is phenotypically plastic.

Tree ring imprints of long-term changes in climate in western Himalaya, India

Abstract: Tree-ring analyses from semi-arid to arid regions in western Himalaya show immense potential for developing millennia long climate records. Millennium and longer ring-width chronologies of Himalayan pencil juniper (Juniperus polycarpos), Himalayan pencil cedar (Cedrus deodara) and Chilgoza pine (Pinus gerardiana) have been developed from different sites in western Himalaya. Studies conducted so far on various conifer species indicate strong precipitation signatures in ring-width measurement series. The paucity of weather records from stations close to tree-ring sampling sites poses difficulty in calibrating tree-ring data against climate data especially precipitation for its strong spatial variability in mountain regions. However, for the existence of strong coherence in temperature, even in data from distant stations, more robust temperature reconstructions representing regional and hemispheric signatures have been developed. Tree-ring records from the region indicate multi-century warm and cool anomalies consistent with the Medieval Warm Period and Little Ice Age anomalies.

Cloning and sequence analysis of putative type II fatty acid synthase genes from Arachis hypogaea L.

Abstract: The cultivated peanut is a valuable source of dietary oil and ranks fifth among the world oil crops. Plant fatty acid biosynthesis is catalysed by type II fatty acid synthase (FAS) in plastids and mitochondria. By constructing a full-length cDNA library derived from immature peanut seeds and homology-based cloning, candidate genes of acyl carrier protein (ACP), malonyl-CoA:ACP transacylase, β-ketoacyl-ACP synthase (I, II, III), β-ketoacyl-ACP reductase, β-hydroxyacyl-ACP dehydrase and enoyl-ACP reductase were isolated. Sequence alignments revealed that primary structures of type II FAS enzymes were highly conserved in higher plants and the catalytic residues were strictly conserved in Escherichia coli and higher plants. Homologue numbers of each type II FAS gene expressing in developing peanut seeds varied from 1 in KASII, KASIII and HD to 5 in ENR. The number of single-nucleotide polymorphisms (SNPs) was quite different in each gene. Peanut type II FAS genes were predicted to target plastids except ACP2 and ACP3. The results suggested that peanut may contain two type II FAS systems in plastids and mitochondria. The type II FAS enzymes in higher plants may have similar functions as those in E. coli.

Relationship among phenotypic plasticity, phenotypic fluctuations, robustness, and evolvability; Waddington’s legacy revisited under the spirit of Einstein

Abstract: Questions on possible relationship between phenotypic plasticity and evolvability, and that between robustness and evolution have been addressed over decades in the field of evolution-development. Based on laboratory evolution experiments and numerical simulations of gene expression dynamics model with an evolving transcription network, we propose quantitative relationships on plasticity, phenotypic fluctuations, and evolvability. By introducing an evolutionary stability assumption on the distribution of phenotype and genotype, the proportionality among phenotypic plasticity against environmental change, variances of phenotype fluctuations of genetic and developmental origins, and evolution speed is obtained. The correlation between developmental robustness to noise and evolutionary robustness to mutation is analysed by simulations of the gene network model. These results provide quantitative formulation on canalization and genetic assimilation, in terms of fluctuations of gene expression levels.

Neurospora as a model fungus for studies in cytogenetics and sexual biology at Stanford.

Abstract: Dodge’s early work (1927–1940) on Neurospora genetics and sexual biology inspired Beadle and Tatum at Stanford to use N. crassa for their landmark discovery that genes specify enzymes. Neurospora has since become a model organism for numerous genetic, cytogenetic, biochemical, molecular and population biology studies. Neurospora is haploid in the vegetative phase with a transient diploid sexual phase. Its meiotic cells (asci) are large, allowing easy examination of dividing nuclei and chromosomes under a light microscope. The haploid meiotic products are themselves the sexual progeny that grow into vegetative cultures, thus avoiding the cumbersome testcrosses and complex dominance-recessive relationships, as in diploid organisms. The Perkins’ laboratory at Stanford (1949–2007) played a pivotal role in advancing our knowledge of Neurospora genetics, sexual biology, cytogenetics and population biology. Since 1974, I have taken advantage of various chromosome-staining methods to examine ascus and ascospore development in wild type and in numerous mutant strains. In addition, I have used GFP-tagged genes to visualize the expression or silencing of unpaired genes in a post-transcriptional gene silencing process (meiotic silencing by unpaired DNA) that operates specifically during meiosis. The genome of N. crassa contains over 10 000 proteincoding genes. Gene knockouts or mutations in specific sequences may now be readily correlated with the observed cytological defects in the sexual stage, thus advancing our molecular understanding of complex processes during ascus and ascospore development.

Correlations between soil microbial and physicochemical variations in a rice paddy: implications for assessing soil health

Abstract: This study was conducted to test the hypothesis that spatial variations in soil microbial variables in a Thai rice paddy are accurately described by multivariate profiles of the soil bacterial communities. We found that community-level physiological profiles of soil bacterial communities could better describe the population density of Rhizoctonia solani in soil than the physicochemical profiles do. However, soil dehydrogenase levels were closely correlated with soil fertility (P<0.05), and these were better described by the physicochemical profiles. Hence, the hypothesis was rejected, and we suspect that soil microbial variables react differently to the same physicochemical changes. The average population density of R. solani (35 colony-forming units/g dry soil) was relatively high in the soil we studied, and the soil fertility was found to be among the poorest in Thailand. The soil quality was comparable to the most degraded bare ground soil in an adjacent bioreserve in terms of Shannon diversity index based on the communitylevel physiological profile as well as values of soil fertility indices. Overall, the soil microbial and physicochemical indicators showed that the paddy soil needs to be supplemented with soil nutrients. Otherwise, R. solani may cause a significant reduction in rice production.

Molecular evolution of the E8 promoter in tomato and some of its relative wild species.

Abstract: The E8 gene is related to ethylene biosynthesis in plants. To explore the effect of the expression pattern of the E8 gene on different E8 promoters, the molecular evolution of E8 promoters was investigated. A total of 16 E8 promoters were cloned from 16 accessions of seven tomato species, and were further analysed. The results from 19 E8 promoters including three previously cloned E8 promoters (X13437, DQ317599 and AF515784) showed that the size of the E8 promoters varied from 2101 bp (LA2150) to 2256 bp (LA2192); their sequences shared 69.9% homology and the average A/T content was 74.9%. Slide-window analysis divided E8 promoters into three regions — A, B and C — and the sequence identity in these regions was 72.5%, 41.2% and 70.8%, respectively. By searching the cis-elements of E8 promoters in the PLACE database, mutant nucleotides were found in some functional elements, and deletions or insertions were also found in regions responsible for ethylene biosysnthesis (−1702 to −1274) and the negative effect region (−1253 to −936). Our results indicate that the size of the functional region for ethylene biosynthesis in the E8 promoter could be shortened from 429 bp to 113 bp (−1612 to −1500). The results of molecular evolution analysis showed that the 19 E8 promoters could be classified into four clade groups, which is basically consistent with evolution of the tomato genome. Southern blot analysis results showed that the copy number of E8 promoters in tomato and some other wild species changed from 1 to 4. Taken together, our study provides important information for further elucidating the E8 gene expression pattern in tomato, analysing functional elements in the E8 promoter and reconstructing the potent E8 promoter.